The following are free sites I frequently use to search for pre-1900 records:
The Church of Jesus Christ of Latter-Day Saints – I particularly like their church records collection.
https://familysearch.org/search
Library and Archives Canada – I often order microfilms of their treaty paylist collection through inter-library loan. I also search online through their School Files Series and Soldiers of the First World War: 1914-1918.
http://www.bac-lac.gc.ca/eng/Pages/home.aspx
Heritage project has digitized copies of Treaty annuity paylists – You would have to know how they are organized to search through them productively. I created my own index from searching through the Library and Archives microfilm collection.
http://heritage.canadiana.ca/view/oocihm.lac_mikan_133552
Manitoba Vital Statistics
http://vitalstats.gov.mb.ca/Query.php
Saskatchewan Vital Statistics
http://genealogy.ehealthsask.ca/vsgs_srch.aspx
BC Archives – Indexes to births (1854-1903), marriages (1872-1940), deaths (1872-1993), colonial marriages (1859-1872) and baptisms (1836-1888).
http://search-collections.royalbcmuseum.bc.ca/Genealogy
HBC Archives – Biographical Sheets
http://www.gov.mb.ca/chc/archives/hbca/biographical/index.html
Automated Genealogy for Canadian censuses: 1901, 1906, 1911
http://automatedgenealogy.com/